Anything you haven't done in Act Two will be locked off in Act Three, and will affect certain events. Fortunately all the important stuff is tied to the Main Girls and the leads so if you've completed all of those then the worst that will happen is a side girl not showing up in Act Three :)
Things that might you might have missed:
1. Jackie, and getting access to Samantha's apartment
2. Getting the two fish girls into the Marina
3. Maxing out your authority in the college
That's all of the somewhat-hidden content I can think of off the top of my head :P